breaking: change internal prec of quip/gap/xyz to float64 (#777)

wanghan-iapcm · Han Wang · web-flow · commit 2905792198f5 · 2025-01-13T18:30:06.000+08:00
&lt;!-- This is an auto-generated comment: release notes by coderabbit.ai
--&gt;

## Summary by CodeRabbit

- **Precision Improvements**
- Updated numpy array data types from `float32` to `float64` for
enhanced numerical precision
- Refined energy and virial value representations in test data files
using scientific notation
  - Removed redundant error handling code

- **Test Data Updates**
- Updated energy value formats in multiple test XYZ files for improved
accuracy

&lt;!-- end of auto-generated comment: release notes by coderabbit.ai --&gt;

Co-authored-by: Han Wang &lt;wang_han@iapcm.ac.cn&gt;
diff --git a/dpdata/xyz/quip_gap_xyz.py b/dpdata/xyz/quip_gap_xyz.py
@@ -161,7 +161,7 @@ def handle_single_xyz_frame(lines):
                         list(filter(bool, field_dict["virial"].split(" ")))
                     ).reshape(3, 3)
                 ]
-            ).astype("float32")
+            ).astype(np.float64)
         else:
             virials = None
 
@@ -175,10 +175,10 @@ def handle_single_xyz_frame(lines):
                     3, 3
                 )
             ]
-        ).astype("float32")
-        info_dict["coords"] = np.array([coords_array]).astype("float32")
-        info_dict["energies"] = np.array([field_dict["energy"]]).astype("float32")
-        info_dict["forces"] = np.array([force_array]).astype("float32")
+        ).astype(np.float64)
+        info_dict["coords"] = np.array([coords_array]).astype(np.float64)
+        info_dict["energies"] = np.array([field_dict["energy"]]).astype(np.float64)
+        info_dict["forces"] = np.array([force_array]).astype(np.float64)
         if virials is not None:
             info_dict["virials"] = virials
         info_dict["orig"] = np.zeros(3)
diff --git a/tests/xyz/xyz_unittest.field.xyz b/tests/xyz/xyz_unittest.field.xyz
@@ -16,7 +16,7 @@ energy=0.2397023e+01    virial="159.582203018    1.23282341824e-05    0.18783516
  
 
   10   
-virial=" -3.68535041825    1.63204257089e-06    -4.28008468355    1.63204257089e-06    18.1630123797    0.0    -4.28008468355    0.0    3.03073243091 "    Lattice=" 9.217080809   0.0   0.0   4.86e-07   6.431267224   0.0   4.201562981   4.1e-08   2.205334915 "  Properties='species:S:1:pos:R:3:Z:I:1:force:R:3 ' energy='-58.342497      '
+virial=" -3.68535041825    1.63204257089e-06    -4.28008468355    1.63204257089e-06    18.1630123797    0.0    -4.28008468355    0.0    3.03073243091 "    Lattice=" 9.217080809   0.0   0.0   4.86e-07   6.431267224   0.0   4.201562981   4.1e-08   2.205334915 "  Properties='species:S:1:pos:R:3:Z:I:1:force:R:3 ' energy='-5.834249877929687500e+01      '
 B   12.38023000000   3.21563000000   2.13103000000   5    -9.35551000000  -0.00000000000  -0.22364600000
 C   12.96783000000   4.32879000000   2.14172000000   6     7.05653600000  11.19171000000   1.80087100000
 C   12.96783000000   2.10247000000   2.14172000000   6     7.05653500000 -11.19171000000   1.80087100000
@@ -28,7 +28,7 @@ C    2.71900000000   1.71197000000   0.17210000000   6    -3.43041200000   0.056
 C    2.71900000000   4.71930000000   0.17210000000   6    -3.43041200000  -0.05665700000  -0.44035700000
 C    9.69981000000   3.21563000000   0.55395000000   6    -2.18778000000  -0.00000000000  -1.00760300000
 10
-energy=-56.397425    virial="-5.61261501333    -6.34809444383e-07    6.34809444383e-07    -6.34809444383e-07    -5.61261501333    6.34809444383e-07    6.34809444383e-07    6.34809444383e-07    4.91130356636"    Lattice="5.512073672   0.0   0.0   4.16e-07   5.512073672   0.0   2.53e-07   2.53e-07   3.347159197"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
+energy=-5.639742660522460938e+01    virial="-5.61261501333    -6.34809444383e-07    6.34809444383e-07    -6.34809444383e-07    -5.61261501333    6.34809444383e-07    6.34809444383e-07    6.34809444383e-07    4.91130356636"    Lattice="5.512073672   0.0   0.0   4.16e-07   5.512073672   0.0   2.53e-07   2.53e-07   3.347159197"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
 B    4.08581000000   4.57623000000   2.94238000000   5     0.03989300000  -1.87257900000   0.97202400000
 C    1.42627000000   0.93584000000   2.94238000000   5    -0.03989300000   1.87257900000   0.97202400000
 C    0.93584000000   4.08581000000   2.94238000000   5     1.87257900000   0.03989300000   0.97202400000
diff --git a/tests/xyz/xyz_unittest.sort.xyz b/tests/xyz/xyz_unittest.sort.xyz
@@ -13,7 +13,7 @@ B    3.19567000000   7.85111000000   1.52250000000   5    -7.25565700000   8.829
 C    2.27564000000   0.00000000000   1.03309000000   6    -0.00000000000  -0.00000000000   0.00000000000
 B    2.27564000000   4.41538000000   1.03309000000   5    -0.00000000000  -0.00000000000   0.00000000000
 10
-energy=-58.342497    virial="-3.68535041825    1.63204257089e-06    -4.28008468355    1.63204257089e-06    18.1630123797    0.0    -4.28008468355    0.0    3.03073243091"    Lattice="9.217080809   0.0   0.0   4.86e-07   6.431267224   0.0   4.201562981   4.1e-08   2.205334915"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
+energy=-5.834249877929687500e+01    virial="-3.68535041825    1.63204257089e-06    -4.28008468355    1.63204257089e-06    18.1630123797    0.0    -4.28008468355    0.0    3.03073243091"    Lattice="9.217080809   0.0   0.0   4.86e-07   6.431267224   0.0   4.201562981   4.1e-08   2.205334915"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
 C   12.96783000000   4.32879000000   2.14172000000   6     7.05653600000  11.19171000000   1.80087100000
 C   12.96783000000   2.10247000000   2.14172000000   6     7.05653500000 -11.19171000000   1.80087100000
 C    7.95424000000   1.03482000000   2.10290000000   6     1.71010500000  -3.80357800000  -0.12402100000
@@ -25,7 +25,7 @@ C    2.71900000000   1.71197000000   0.17210000000   6    -3.43041200000   0.056
 C    2.71900000000   4.71930000000   0.17210000000   6    -3.43041200000  -0.05665700000  -0.44035700000
 C    9.69981000000   3.21563000000   0.55395000000   6    -2.18778000000  -0.00000000000  -1.00760300000
 10
-energy=-56.397425    virial="-5.61261501333    -6.34809444383e-07    6.34809444383e-07    -6.34809444383e-07    -5.61261501333    6.34809444383e-07    6.34809444383e-07    6.34809444383e-07    4.91130356636"    Lattice="5.512073672   0.0   0.0   4.16e-07   5.512073672   0.0   2.53e-07   2.53e-07   3.347159197"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
+energy=-5.639742660522460938e+01    virial="-5.61261501333    -6.34809444383e-07    6.34809444383e-07    -6.34809444383e-07    -5.61261501333    6.34809444383e-07    6.34809444383e-07    6.34809444383e-07    4.91130356636"    Lattice="5.512073672   0.0   0.0   4.16e-07   5.512073672   0.0   2.53e-07   2.53e-07   3.347159197"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
 B    4.08581000000   4.57623000000   2.94238000000   5     0.03989300000  -1.87257900000   0.97202400000
 C    1.42627000000   0.93584000000   2.94238000000   5    -0.03989300000   1.87257900000   0.97202400000
 C    0.93584000000   4.08581000000   2.94238000000   5     1.87257900000   0.03989300000   0.97202400000
diff --git a/tests/xyz/xyz_unittest.xyz b/tests/xyz/xyz_unittest.xyz
@@ -13,7 +13,7 @@ C    2.27564000000   1.56002000000   1.03309000000   6    -0.00000000000  -4.519
 C    2.27564000000   7.27074000000   1.03309000000   6     0.00000000000   4.51935800000   0.00000000000
 C    2.27564000000   0.00000000000   1.03309000000   6    -0.00000000000  -0.00000000000   0.00000000000
 10
-energy=-58.342497    virial="-3.68535041825    1.63204257089e-06    -4.28008468355    1.63204257089e-06    18.1630123797    0.0    -4.28008468355    0.0    3.03073243091"    Lattice="9.217080809   0.0   0.0   4.86e-07   6.431267224   0.0   4.201562981   4.1e-08   2.205334915"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
+energy=-5.834249877929687500e+01    virial="-3.68535041825    1.63204257089e-06    -4.28008468355    1.63204257089e-06    18.1630123797    0.0    -4.28008468355    0.0    3.03073243091"    Lattice="9.217080809   0.0   0.0   4.86e-07   6.431267224   0.0   4.201562981   4.1e-08   2.205334915"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
 B   12.38023000000   3.21563000000   2.13103000000   5    -9.35551000000  -0.00000000000  -0.22364600000
 C   12.96783000000   4.32879000000   2.14172000000   6     7.05653600000  11.19171000000   1.80087100000
 C   12.96783000000   2.10247000000   2.14172000000   6     7.05653500000 -11.19171000000   1.80087100000
@@ -25,7 +25,7 @@ C    2.71900000000   1.71197000000   0.17210000000   6    -3.43041200000   0.056
 C    2.71900000000   4.71930000000   0.17210000000   6    -3.43041200000  -0.05665700000  -0.44035700000
 C    9.69981000000   3.21563000000   0.55395000000   6    -2.18778000000  -0.00000000000  -1.00760300000
 10
-energy=-56.397425    virial="-5.61261501333    -6.34809444383e-07    6.34809444383e-07    -6.34809444383e-07    -5.61261501333    6.34809444383e-07    6.34809444383e-07    6.34809444383e-07    4.91130356636"    Lattice="5.512073672   0.0   0.0   4.16e-07   5.512073672   0.0   2.53e-07   2.53e-07   3.347159197"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
+energy=-5.639742660522460938e+01    virial="-5.61261501333    -6.34809444383e-07    6.34809444383e-07    -6.34809444383e-07    -5.61261501333    6.34809444383e-07    6.34809444383e-07    6.34809444383e-07    4.91130356636"    Lattice="5.512073672   0.0   0.0   4.16e-07   5.512073672   0.0   2.53e-07   2.53e-07   3.347159197"     Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
 B    4.08581000000   4.57623000000   2.94238000000   5     0.03989300000  -1.87257900000   0.97202400000
 C    1.42627000000   0.93584000000   2.94238000000   5    -0.03989300000   1.87257900000   0.97202400000
 C    0.93584000000   4.08581000000   2.94238000000   5     1.87257900000   0.03989300000   0.97202400000

Original file line number	Diff line number	Diff line change
`@@ -16,7 +16,7 @@ energy=0.2397023e+01 virial="159.582203018 1.23282341824e-05 0.18783516`
`16`	`16`
`17`	`17`
`18`	`18`	`10`
`19`		`-virial=" -3.68535041825 1.63204257089e-06 -4.28008468355 1.63204257089e-06 18.1630123797 0.0 -4.28008468355 0.0 3.03073243091 " Lattice=" 9.217080809 0.0 0.0 4.86e-07 6.431267224 0.0 4.201562981 4.1e-08 2.205334915 " Properties='species:S:1:pos:R:3:Z:I:1:force:R:3 ' energy='-58.342497 '`
	`19`	`+virial=" -3.68535041825 1.63204257089e-06 -4.28008468355 1.63204257089e-06 18.1630123797 0.0 -4.28008468355 0.0 3.03073243091 " Lattice=" 9.217080809 0.0 0.0 4.86e-07 6.431267224 0.0 4.201562981 4.1e-08 2.205334915 " Properties='species:S:1:pos:R:3:Z:I:1:force:R:3 ' energy='-5.834249877929687500e+01 '`
`20`	`20`	`B 12.38023000000 3.21563000000 2.13103000000 5 -9.35551000000 -0.00000000000 -0.22364600000`
`21`	`21`	`C 12.96783000000 4.32879000000 2.14172000000 6 7.05653600000 11.19171000000 1.80087100000`
`22`	`22`	`C 12.96783000000 2.10247000000 2.14172000000 6 7.05653500000 -11.19171000000 1.80087100000`
`@@ -28,7 +28,7 @@ C 2.71900000000 1.71197000000 0.17210000000 6 -3.43041200000 0.056`
`28`	`28`	`C 2.71900000000 4.71930000000 0.17210000000 6 -3.43041200000 -0.05665700000 -0.44035700000`
`29`	`29`	`C 9.69981000000 3.21563000000 0.55395000000 6 -2.18778000000 -0.00000000000 -1.00760300000`
`30`	`30`	`10`
`31`		`-energy=-56.397425 virial="-5.61261501333 -6.34809444383e-07 6.34809444383e-07 -6.34809444383e-07 -5.61261501333 6.34809444383e-07 6.34809444383e-07 6.34809444383e-07 4.91130356636" Lattice="5.512073672 0.0 0.0 4.16e-07 5.512073672 0.0 2.53e-07 2.53e-07 3.347159197" Properties=species:S:1:pos:R:3:Z:I:1:force:R:3`
	`31`	`+energy=-5.639742660522460938e+01 virial="-5.61261501333 -6.34809444383e-07 6.34809444383e-07 -6.34809444383e-07 -5.61261501333 6.34809444383e-07 6.34809444383e-07 6.34809444383e-07 4.91130356636" Lattice="5.512073672 0.0 0.0 4.16e-07 5.512073672 0.0 2.53e-07 2.53e-07 3.347159197" Properties=species:S:1:pos:R:3:Z:I:1:force:R:3`
`32`	`32`	`B 4.08581000000 4.57623000000 2.94238000000 5 0.03989300000 -1.87257900000 0.97202400000`
`33`	`33`	`C 1.42627000000 0.93584000000 2.94238000000 5 -0.03989300000 1.87257900000 0.97202400000`
`34`	`34`	`C 0.93584000000 4.08581000000 2.94238000000 5 1.87257900000 0.03989300000 0.97202400000`